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Run nesting and the new physics using the global-workflow #4

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Run nesting and the new physics using the global-workflow #4

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d50754d
add parm/config/global-nest, links from ../gfs
guoqing-noaa Apr 19, 2024
e3c85ff
config.ufs, config.fcst: change from links to regular files
guoqing-noaa Apr 19, 2024
a6ec298
update parameters for the global_nest_v1 physics in config.fcst and c…
guoqing-noaa Apr 19, 2024
7e7fe2c
update ush/parsing_namelists_FV3.sh to include the FV3_global_nest op…
guoqing-noaa Apr 19, 2024
c0208ef
add parm/ufs/fv3/field_table_thompson_aero_tke_progsigma
guoqing-noaa Apr 19, 2024
c454e77
use the new use the new field_table_thompson_aero_tke_progsigma for g…
guoqing-noaa Apr 19, 2024
936e484
Merge pull request #3 from guoqing-noaa/ccpp-global-nest
guoqing-noaa Apr 19, 2024
60d7d83
modify config.fcst to set DO_CA=NO
guoqing-noaa Apr 20, 2024
f89540c
simplify the DO_CA change in config.fcst
guoqing-noaa Apr 20, 2024
5d51776
update config.stage_ic to include UFS-AR ICs
guoqing-noaa Apr 20, 2024
f8af477
set the MPI layout for the nested tile
guoqing-noaa Apr 20, 2024
cc7dcd6
add the 'DO_NEST' variable in config.base
guoqing-noaa Apr 20, 2024
85b12e7
update config.ufs for DO_NEST
guoqing-noaa Apr 20, 2024
1d83e88
update exglobal_stage_ic.sh for DO_NEST
guoqing-noaa Apr 20, 2024
e5315c9
add one comment line about compiling with -DFASTER=ON in build_ufs.sh
guoqing-noaa Apr 20, 2024
91151af
update forecast_postdet.sh
guoqing-noaa Apr 20, 2024
4be24e5
update forecast_predet.sh
guoqing-noaa Apr 20, 2024
eb4cfe2
update parsing_namelists_FV3.sh
guoqing-noaa Apr 20, 2024
023e510
update parsing_model_configure_FV3.sh
guoqing-noaa Apr 20, 2024
d207862
add fix.nest.ver for DO_NEST
guoqing-noaa Apr 20, 2024
2bedcf3
simlify fix.nest.ver
guoqing-noaa Apr 20, 2024
63447b3
add ush/global_nest_patch.sh
guoqing-noaa Apr 20, 2024
273a08a
minor bug fix in versions/fix.nest.ver
guoqing-noaa Apr 20, 2024
fd169d3
bug fix on config.base
guoqing-noaa Apr 20, 2024
84c249c
put changes to config/gfs/config.ufs
guoqing-noaa Apr 20, 2024
7b2f01f
merge changes to config/gfs/config.fcst
guoqing-noaa Apr 20, 2024
86de796
remove global-nest
guoqing-noaa Apr 20, 2024
409543b
different parameter settings are now based on CCPP_SUITE not DO_NEST
guoqing-noaa Apr 20, 2024
bbc0e55
update sorc/ufs_model.fd
guoqing-noaa Apr 20, 2024
dd37f80
Update parm/config/gfs/config.ufs
guoqing-noaa Apr 22, 2024
469a63c
changes based on suggestions
guoqing-noaa Apr 23, 2024
53da372
remove global_nest_patch.sh
guoqing-noaa Apr 23, 2024
7c2dbaf
change case prefix to GLOBAL-NEST
guoqing-noaa Apr 23, 2024
623c196
remove sorc/tmp.sh
guoqing-noaa Apr 24, 2024
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8 changes: 8 additions & 0 deletions parm/config/gfs/config.base
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Original file line number Diff line number Diff line change
Expand Up @@ -184,6 +184,14 @@ export DO_AERO="NO"
export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
export DOBNDPNT_WAVE="NO"
export FRAC_GRID=".true."
export DO_NEST="NO" # Whether to run a global-nested domain
if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
export ntiles=7
export NEST_OUTPUT_GRID="regional_latlon"
else
export ntiles=6
export NEST_OUTPUT_GRID=""
fi

# Set operational resolution
export OPS_RES="C768" # Do not change # TODO: Why is this needed and where is it used?
Expand Down
26 changes: 24 additions & 2 deletions parm/config/gfs/config.fcst
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Expand Up @@ -135,7 +135,11 @@ fi

# PBL/turbulance schemes
export hybedmf=".false."
export satmedmf=".true."
if [[ "${CCPP_SUITE}" == "FV3_global_nest"* ]]; then
export satmedmf=".false."
else
export satmedmf=".true."
fi
export isatmedmf=1
tbf=""
if [[ "${satmedmf}" == ".true." ]]; then tbf="_satmedmf" ; fi
Expand Down Expand Up @@ -207,6 +211,20 @@ case ${imp_physics} in
export nord=2
export dddmp=0.1
export d4_bg=0.12

if [[ "${CCPP_SUITE}" == "FV3_global_nest"* ]]; then
export FIELD_TABLE="${PARMgfs}/ufs/fv3/field_table_thompson_aero_tke${tbp}"
export ltaerosol=".true."
export lcnorm=".true."
export do_mynnedmf=".true."
export do_mynnsfclay=".true."
export imfshalcnv=5
export imfdeepcnv=5
export betascu=0.5
export betamcu=1.5
export betadcu=8.0
fi

;;
11) # GFDL
export ncld=5
Expand Down Expand Up @@ -235,7 +253,11 @@ export DO_SPPT=${DO_SPPT:-"NO"}
export DO_SKEB=${DO_SKEB:-"NO"}
export DO_SHUM=${DO_SHUM:-"NO"}
export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
export DO_CA=${DO_CA:-"YES"}
if [[ "${DO_NEST:-NO}" == YES ]] ; then
export DO_CA="NO" #CA does not work with nesting.
else
export DO_CA=${DO_CA:-"YES"}
fi

#coupling settings
export cplmode="ufs.frac"
Expand Down
7 changes: 7 additions & 0 deletions parm/config/gfs/config.resources
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Expand Up @@ -586,6 +586,13 @@ case ${step} in
[[ "${DO_ICE}" == "YES" ]] && nthreads_cice6=1
fi

if [[ ${ntiles} -gt 6 ]] ; then
export layout_x_nest=${layout_x_nest:-10}
export layout_y_nest=${layout_y_nest:-10}
export npx_nest=${npx_nest:-1441}
export npy_nest=${npy_nest:-961}
fi

# PETS for the atmosphere dycore
(( FV3PETS = ntasks_fv3 * nthreads_fv3 ))
echo "FV3 using (nthreads, PETS) = (${nthreads_fv3}, ${FV3PETS})"
Expand Down
4 changes: 4 additions & 0 deletions parm/config/gfs/config.stage_ic
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Expand Up @@ -38,4 +38,8 @@ case "${CASE}" in
;;
esac

if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
export CPL_ATMIC=UFS-AR_${CASE}
fi

echo "END: config.stage_ic"
99 changes: 99 additions & 0 deletions parm/config/gfs/config.ufs
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,21 @@ if [[ "${skip_mom6}" == "false" ]] || [[ "${skip_cice6}" == "false" ]] || [[ "${
skip_mediator=false
fi

if [[ "${DO_NEST:-NO}" == YES ]] ; then
export grid_type=0
export target_lat=32.5
export target_lon=-135.0
export stretch_fac=1.0001
export NEST_LON1=-195.000000
export NEST_LAT1=-7.500000
export NEST_LON2=-75.000000
export NEST_LAT2=72.500000
export twowaynest=${twowaynest:-.true.}
else
# No nest.
export grid_type=-1
fi

# (Standard) Model resolution dependent variables
case "${fv3_res}" in
"C48")
Expand Down Expand Up @@ -105,6 +120,24 @@ case "${fv3_res}" in
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=1
export WRITE_GROUP_GFS=1
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=1
if [[ ${DO_NEST:-NO} == YES ]] ; then
export DELTIM=450
export layout_x_gfs=4
export layout_y_gfs=4
export layout_x_nest=12
export layout_y_nest=10
export nest_refine=4
export nest_ioffset=4
export nest_joffset=9
export npx_nest=361
export npy_nest=241
export NEST_DLON=0.25
export NEST_DLAT=0.25
export WRITE_GROUP=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=2
export WRITE_GROUP_GFS=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=2
fi
;;
"C192")
export DELTIM=450
Expand All @@ -123,6 +156,24 @@ case "${fv3_res}" in
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
export WRITE_GROUP_GFS=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=5
if [[ ${DO_NEST:-NO} == YES ]] ; then
export DELTIM=225
export layout_x_gfs=5
export layout_y_gfs=6
export layout_x_nest=15
export layout_y_nest=25
export nest_refine=4
export nest_ioffset=7
export nest_joffset=19
export npx_nest=721
export npy_nest=481
export NEST_DLON=0.125
export NEST_DLAT=0.125
export WRITE_GROUP=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=15
export WRITE_GROUP_GFS=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=15
fi
;;
"C384")
export DELTIM=300
Expand All @@ -141,6 +192,26 @@ case "${fv3_res}" in
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
export WRITE_GROUP_GFS=4
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=10
if [[ ${DO_NEST:-NO} == YES ]] ; then
export DELTIM=150
export layout_x=8
export layout_y=8
export layout_x_gfs=8
export layout_y_gfs=8
export layout_x_nest=34
export layout_y_nest=24
export nest_refine=4
export nest_ioffset=13
export nest_joffset=37
export npx_nest=1441
export npy_nest=961
export NEST_DLON=0.0625
export NEST_DLAT=0.0625
export WRITE_GROUP=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=20
export WRITE_GROUP_GFS=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
fi
;;
"C768")
export DELTIM=150
Expand All @@ -159,6 +230,28 @@ case "${fv3_res}" in
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
export WRITE_GROUP_GFS=4
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
if [[ ${DO_NEST:-NO} == YES ]] ; then
export DELTIM=75
export layout_x=16
export layout_y=10
export layout_x_gfs=16
export layout_y_gfs=10
export layout_x_nest=48
export layout_y_nest=45
export nthreads_fv3=2
export nthreads_fv3_gfs=2
export nest_refine=4
export nest_ioffset=24
export nest_joffset=72
export npx_nest=2881
export npy_nest=1921
export NEST_DLON=0.0325
export NEST_DLAT=0.0325
export WRITE_GROUP=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=90
export WRITE_GROUP_GFS=2
export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=90
fi
;;
"C1152")
export DELTIM=120
Expand Down Expand Up @@ -209,6 +302,9 @@ export WRTTASK_PER_GROUP_PER_THREAD_GFS

(( ntasks_fv3 = layout_x * layout_y * 6 ))
(( ntasks_fv3_gfs = layout_x_gfs * layout_y_gfs * 6 ))
if [[ "${DO_NEST:-NO}" == YES ]] ; then
(( ntasks_fv3_gfs += layout_x_nest * layout_y_nest ))
fi
export ntasks_fv3
export ntasks_fv3_gfs

Expand Down Expand Up @@ -242,6 +338,9 @@ export cplchm=".false."
export cplwav=".false."
export cplwav2atm=".false."
export CCPP_SUITE="FV3_GFS_v17_p8_ugwpv1"
if [[ "${DO_NEST:-NO}" == YES ]] ; then
export CCPP_SUITE="FV3_global_nest_v1"
fi
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model_list="atm"

# Mediator specific settings
Expand Down
70 changes: 70 additions & 0 deletions parm/ufs/fv3/field_table_thompson_aero_tke_progsigma
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@@ -0,0 +1,70 @@
# added by FRE: sphum must be present in atmos
# specific humidity for moist runs
"TRACER", "atmos_mod", "sphum"
"longname", "specific humidity"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=3.e-6" /
# prognostic cloud water mixing ratio
"TRACER", "atmos_mod", "liq_wat"
"longname", "cloud water mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic ice water mixing ratio
"TRACER", "atmos_mod", "ice_wat"
"longname", "cloud ice mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic rain water mixing ratio
"TRACER", "atmos_mod", "rainwat"
"longname", "rain water mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic snow water mixing ratio
"TRACER", "atmos_mod", "snowwat"
"longname", "snow water mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic Grau water mixing ratio
"TRACER", "atmos_mod", "graupel"
"longname", "graupel mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic cloud water number concentration
"TRACER", "atmos_mod", "water_nc"
"longname", "cloud liquid water number concentration"
"units", "/kg"
"profile_type", "fixed", "surface_value=0.0" /
# prognostic cloud ice number concentration
"TRACER", "atmos_mod", "ice_nc"
"longname", "cloud ice water number concentration"
"units", "/kg"
"profile_type", "fixed", "surface_value=0.0" /
# prognostic rain number concentration
"TRACER", "atmos_mod", "rain_nc"
"longname", "rain number concentration"
"units", "/kg"
"profile_type", "fixed", "surface_value=0.0" /
# prognostic ozone mixing ratio tracer
"TRACER", "atmos_mod", "o3mr"
"longname", "ozone mixing ratio"
"units", "kg/kg"
"profile_type", "fixed", "surface_value=1.e30" /
# prognostic sigmab tracer
"TRACER", "atmos_mod", "sigmab"
"longname", "sigma fraction"
"units", "fraction"
"profile_type", "fixed", "surface_value=0.0" /
# water- and ice-friendly aerosols (Thompson)
"TRACER", "atmos_mod", "liq_aero"
"longname", "water-friendly aerosol number concentration"
"units", "/kg"
"profile_type", "fixed", "surface_value=0.0" /
"TRACER", "atmos_mod", "ice_aero"
"longname", "ice-friendly aerosol number concentration"
"units", "/kg"
"profile_type", "fixed", "surface_value=0.0" /
# prognostic subgrid scale turbulent kinetic energy
"TRACER", "atmos_mod", "sgs_tke"
"longname", "subgrid scale turbulent kinetic energy"
"units", "m2/s2"
"profile_type", "fixed", "surface_value=0.0" /
13 changes: 10 additions & 3 deletions scripts/exglobal_stage_ic.sh
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Expand Up @@ -42,9 +42,13 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
err=$((err + rc))
done
for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
for ((tt = 1; tt <= 6; tt++)); do
for ((tt = 1; tt <= ntiles; tt++)); do
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
if (( tt > 6 )) ; then
tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.nest0$((tt-5)).tile${tt}.nc"
else
tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
fi
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
Expand All @@ -62,14 +66,17 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
for ftype in gfs_data sfc_data; do
for ((tt = 1; tt <= 6; tt++)); do
for ((tt = 1; tt <= ntiles; tt++)); do
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
done
if (( ntiles > 6 )); then
${NLN} "${COM_ATMOS_INPUT}/${ftype}.tile7.nc" "${COM_ATMOS_INPUT}/${ftype}.nest02.tile7.nc"
fi
done
fi

Expand Down
2 changes: 2 additions & 0 deletions sorc/build_ufs.sh
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Expand Up @@ -32,6 +32,8 @@ source "./tests/module-setup.sh"
MAKE_OPT="-DAPP=${APP} -D32BIT=ON -DCCPP_SUITES=${CCPP_SUITES}"
[[ ${PDLIB:-"OFF"} = "ON" ]] && MAKE_OPT+=" -DPDLIB=ON"
[[ ${BUILD_TYPE:-"Release"} = "Debug" ]] && MAKE_OPT+=" -DDEBUG=ON"
#MAKE_OPT+=" -DFASTER=ON" #comment out this line for the global_nest runs

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This should have been left in as a -f command line option. Users should not edit the build scripts and uncomment things.

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-f command line option can be easily passed into build_ufs.sh but it is hard to be passed into build_all.sh
We will consider a full workflow instead of only the forecast part.
Users need to modify build_ufs.sh anyway to include the global_nest_v1 physics in the compiling time.

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In that case, it is best to use -DFASTER=ON as the default. It was designed to be both faster and safer than the defaults.

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I trust you. But I am not sure whether EMC will accept a default -DFASTER=ON. But we can try.

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The best option is to have -f in build_all.sh and have it passed down. If you don't want to do that, we should have it be -DFASTER=ON by default. Then EMC will tell us how to make it optional in the review.

COMPILE_NR=0
CLEAN_BEFORE=YES
CLEAN_AFTER=NO
Expand Down
2 changes: 1 addition & 1 deletion sorc/ufs_model.fd
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Submodule ufs_model.fd updated 77 files
+24 −17 .github/workflows/aux.yml
+37 −0 .github/workflows/superlinter.yml
+16 −0 .shellcheckrc
+1 −1 CICE-interface/CICE
+1 −1 CICE-interface/CMakeLists.txt
+1 −1 CMEPS-interface/CMEPS
+1 −1 FV3
+1 −1 MOM6-interface/MOM6
+4 −3 NOAHMP-interface/CMakeLists.txt
+1 −1 NOAHMP-interface/noahmp
+1 −1 WW3
+16 −8 build.sh
+7 −1 cmake/Intel.cmake
+1 −1 doc/UsersGuide/requirements.txt
+624 −5 doc/UsersGuide/source/Configurations.rst
+13 −13 doc/UsersGuide/source/FAQ.rst
+1 −1 doc/UsersGuide/source/InputsOutputs.rst
+3 −1 doc/UsersGuide/source/Introduction.rst
+6 −3 doc/UsersGuide/source/conf.py
+1 −1 stochastic_physics
+76 −8 tests/atparse.bash
+1 −1 tests/bl_date.conf
+103 −101 tests/ci/repo_check.sh
+49 −48 tests/compile.sh
+1,582 −1,431 tests/default_vars.sh
+10 −7 tests/fv3_conf/compile_slurm.IN_hera
+13 −9 tests/fv3_conf/fv3_slurm.IN_hera
+24 −24 tests/logs/OpnReqTests_control_p8_hera.log
+12 −12 tests/logs/OpnReqTests_cpld_control_nowave_noaero_p8_hera.log
+12 −12 tests/logs/OpnReqTests_regional_control_hera.log
+272 −263 tests/logs/RegressionTests_acorn.log
+340 −278 tests/logs/RegressionTests_derecho.log
+274 −286 tests/logs/RegressionTests_gaea.log
+368 −370 tests/logs/RegressionTests_hera.log
+365 −457 tests/logs/RegressionTests_hercules.log
+244 −256 tests/logs/RegressionTests_jet.log
+277 −369 tests/logs/RegressionTests_orion.log
+235 −249 tests/logs/RegressionTests_wcoss2.log
+11 −11 tests/module-setup.sh
+1 −1 tests/opnReqTest
+57 −44 tests/parm/ice_in.IN
+5 −4 tests/parm/ufs.configure.atm_lnd.IN
+2 −2 tests/parm/ufs.configure.atmw.IN
+3 −2 tests/parm/ufs.configure.hafs_atm_docn.IN
+3 −2 tests/parm/ufs.configure.hafs_atm_ocn.IN
+3 −2 tests/parm/ufs.configure.hafs_atm_ocn_wav.IN
+3 −2 tests/parm/ufs.configure.hafs_atm_ocn_wav_inline.IN
+2 −1 tests/parm/ufs.configure.hafs_atm_ocn_wav_mom6.IN
+3 −2 tests/parm/ufs.configure.hafs_atm_wav.IN
+2 −2 tests/parm/ufs.configure.s2s.IN
+2 −2 tests/parm/ufs.configure.s2s_aoflux_esmf.IN
+2 −2 tests/parm/ufs.configure.s2s_esmf.IN
+2 −2 tests/parm/ufs.configure.s2sa.IN
+2 −2 tests/parm/ufs.configure.s2sa_esmf.IN
+2 −2 tests/parm/ufs.configure.s2sw.IN
+2 −2 tests/parm/ufs.configure.s2sw_esmf.IN
+2 −2 tests/parm/ufs.configure.s2sw_fast_esmf.IN
+2 −2 tests/parm/ufs.configure.s2swa.IN
+2 −2 tests/parm/ufs.configure.s2swa_esmf.IN
+2 −2 tests/parm/ufs.configure.s2swa_fast_esmf.IN
+1 −1 tests/rt.conf
+752 −573 tests/rt.sh
+374 −300 tests/rt_utils.sh
+32 −37 tests/run_compile.sh
+162 −144 tests/run_test.sh
+13 −0 tests/test_changes.list
+0 −1 tests/tests/atmwav_control_noaero_p8
+0 −1 tests/tests/cpld_bmark_p8
+0 −1 tests/tests/cpld_bmark_p8_35d
+0 −2 tests/tests/cpld_control_c192_p8
+0 −1 tests/tests/cpld_control_c48
+1 −1 tests/tests/cpld_debug_pdlib_p8
+0 −1 tests/tests/cpld_restart_bmark_p8
+0 −1 tests/tests/cpld_restart_c192_p8
+0 −1 tests/tests/cpld_restart_c48
+0 −1 tests/tests/cpld_warmstart_c48
+1 −0 tests/tests/regional_atmaq_debug
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